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Pirnajmedin F, Majidi MM, Jaškūnė K. Adaptive strategies to drought stress in grasses of the poaceae family under climate change: Physiological, genetic and molecular perspectives: A review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108814. [PMID: 38875780 DOI: 10.1016/j.plaphy.2024.108814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024]
Abstract
Drought stress is one of the most critical abiotic factors which negatively impacts on growth, productivity, and survival of plants. Grass species have an important role in the sustainable intensification of cropping systems. This review focus on the specific drought tolerance characteristics in grass species and application of prevalent classical and molecular methods for genetic improvement of them to drought stress. Generally, grass species adapt to drought stress by utilizing more than one strategy including of changes in the root growth, photosynthetic pigments, activation of antioxidant enzymes, and accumulation of compatible osmolytes. They also have other specific characteristics consisted of summer dormancy, drought recovery, and persistence, which lead to drought adaptation after prolonged drought. Studies on different grasses, indicated that most of above mentioned traits usually have positive correlation with drought tolerance. Also, high heritability has been reported for most of them in different grasses. Therefore, an effective index might be considering in identification of drought tolerance genotypes. Recently, high-throughput imaging phenotyping and advanced molecular techniques such as genotyping-by-sequencing (GBS), RNA sequencing, genome-wide association study, and genome editing help conventional breeding methods to increase the accuracy, selection efficiency, genetic gains, and speed of breeding programs for developing drought tolerant cultivars.
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Affiliation(s)
- Fatemeh Pirnajmedin
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Mohammad Mahdi Majidi
- Plant Genetics and Breeding, Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Kristina Jaškūnė
- Laboratory of Genetics and Physiology, Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Lithuania.
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Hatami Maleki H, Mohammadi R, Firouzkuhi F, Darvishzadeh R, Zeinalzadeh-Tabrizi H. Molecular evidence depicts genetic divergence among Agropyron elongatum and A. cristatum accessions from gene pool of Iran. PLoS One 2023; 18:e0294694. [PMID: 38033138 PMCID: PMC10688953 DOI: 10.1371/journal.pone.0294694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
The genus Agropyron has an important role in soil protection and forage production in rangelands. The investigation utilized 37 ISSR primers, resulting in the detection of 956 loci within the A. elongatum genome and 705 loci within the A. cristatum genome. The findings revealed a high level of polymorphism, with 97% of loci in A. elongatum and 84% of loci in A. cristatum exhibiting variability. Notably, the primer (AC)8GCT emerged as a promising candidate for evaluating genetic diversity due to its ability to amplify numerous loci in both species. Using both the UPGMA algorithm and Bayesian analysis, the examined Agropyron accessions were categorized into two subgroups based on their respective species. The Q values associated with these subgroups suggested that certain accessions, namely "G16," "G19," "G20," "G21," "G22," "G23," "G24," and "G25," displayed potential admixture genomes. An analysis of molecular variance (AMOVA) underscored the significance of within-species variability, which accounted for 69% of the overall diversity, compared to between-species variability at 31%. Various genetic diversity parameters, including Na, Ne, I, He, and the number of private loci, were found to be higher in A. elongatum when compared to A. cristatum. Furthermore, Jaccard similarity coefficients ranged from 0.33 to 0.66 in A. cristatum and from 0.25 to 0.7 in A. elongatum, indicating the extent of genetic relatedness among these species. Intriguingly, the study identified two and three heterotic groups in A. cristatum and A. elongatum, respectively, which could be harnessed in the development of synthetic varieties to exploit heterosis. The results also indicated that a small proportion of ISSR loci pairs (5.2% in A. elongatum and 0.5% in A. cristatum) exhibited significant levels of linkage disequilibrium (LD) (P≤0.05), suggesting the potential utility of LD-based association mapping in Agropyron species. In conclusion, this research sheds light on the genetic diversity of Agropyron species and provides valuable insights into their potential applications in soil protection and forage production, as well as the prospects for enhancing genetic variability and heterosis in these species.
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Affiliation(s)
- Hamid Hatami Maleki
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Reza Mohammadi
- Branch for Northwest & West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran
| | - Fatemeh Firouzkuhi
- Department of Plant Production and Genetics, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Reza Darvishzadeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hossein Zeinalzadeh-Tabrizi
- Department of Horticulture and Agronomy, Faculty of Agriculture, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
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Tang W, Dong Z, Gao L, Wang X, Li T, Sun C, Chu Z, Cui D. Genetic diversity and population structure of modern wheat (Triticum aestivum L.) cultivars in Henan Province of China based on SNP markers. BMC PLANT BIOLOGY 2023; 23:542. [PMID: 37924000 PMCID: PMC10625233 DOI: 10.1186/s12870-023-04537-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Henan is the province with the greatest wheat production in China. Although more than 100 cultivars are used for production, many cultivars are still insufficient in quality, disease resistance, adaptability and yield potential. To overcome these limitations, it is necessary to constantly breed new cultivars to maintain the continuous and stable growth of wheat yield and quality. To improve breeding efficiency, it is important to evaluate the genetic diversity and population genetic structure of its cultivars. However, there are no such reports from Henan Province. Therefore, in this study, single nucleotide polymorphism (SNP) markers were used to study the population genetic structure and genetic diversity of 243 wheat cultivars included in a comparative test of wheat varieties in Henan Province, aiming to provide a reference for the utilization of backbone parents and the selection of hybrid combinations in the genetic improvement of wheat cultivars. RESULTS In this study, 243 wheat cultivars from Henan Province of China were genotyped by the Affymetrix Axiom Wheat660K SNP chip, and 21 characteristics were investigated. The cultivars were divided into ten subgroups; each subgroup had distinct characteristics and unique utilization value. Furthermore, based on principal component analysis, Zhoumai cultivars were the main hybrid parents, followed by Aikang 58, high-quality cultivars, and Shandong cultivars. Genetic diversity analysis showed that 61.3% of SNPs had a high degree of genetic differentiation, whereas 33.4% showed a moderate degree. The nucleotide diversity of subgenome B was relatively high, with an average π value of 3.91E-5; the nucleotide diversity of subgenome D was the lowest, with an average π value of 2.44E-5. CONCLUSION The parents used in wheat cross-breeding in Henan Province are similar, with a relatively homogeneous genetic background and low genetic diversity. These results will not only contribute to the objective evaluation and utilization of the tested cultivars but also provide insights into the current conditions and existing challenges of wheat cultivar breeding in Henan Province, thereby facilitating the scientific formulation of breeding objectives and strategies to improve breeding efficiency.
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Affiliation(s)
- Wenjing Tang
- College of Agronomy/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046, China
- Henan Agricultural Remote Sensing Monitoring Center, Zhengzhou, 450002, China
| | - Zhongdong Dong
- College of Agronomy/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046, China
| | - Lifeng Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xicheng Wang
- Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Tianbao Li
- College of Agronomy/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046, China
| | - Congwei Sun
- College of Agronomy/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zongli Chu
- College of Agronomy, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Dangqun Cui
- College of Agronomy/Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450046, China.
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Al Salameen F, Habibi N, Al Amad S, Al Doaij B. Genetic Diversity of Rhanterium eppaposum Oliv. Populations in Kuwait as Revealed by GBS. PLANTS (BASEL, SWITZERLAND) 2022; 11:1435. [PMID: 35684208 PMCID: PMC9183190 DOI: 10.3390/plants11111435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/14/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Natural populations of Rhanterium eppaposum Oliv. (Arfaj), a perennial forage shrub, have depleted due to unethical human interventions and climate change in Kuwait. Therefore, there is an urgent need to conserve this native plant through the assessment of its genetic diversity and population structure. Genotyping by sequencing (GBS) has recently emerged as a powerful tool for the molecular diversity analysis of higher plants without prior knowledge of their genome. This study represents the first effort in using GBS to discover genome-wide single nucleotide polymorphisms (SNPs) of local Rhanterium plants to assess the genetic diversity present in landraces collected from six different locations in Kuwait. The study generated a novel set of 11,231 single nucleotide polymorphisms (SNPs) and indels (insertions and deletions) in 98 genotypes of Rhanterium. The analysis of molecular variance (AMOVA) revealed ~1.5% variation residing among the six populations, ~5% among the individuals within the population and 93% variation present within the populations (FST = 0.029; p = 0.0). Bayesian and UPGMA analyses identified two admixed clusters of the tested samples; however, the principal coordinates analysis returned the complete population as a single group. Mantel's test returned a very weak correlation coefficient of r2 = 0.101 (p = 0.00) between the geographic and genetic distance. These findings are useful for the native species to formulate conservation strategies for its sustainable management and desert rehabilitation.
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Affiliation(s)
| | - Nazima Habibi
- Environment and Life Science Research Centre, Kuwait Institute for Scientific Research, Safat 13109, Kuwait; (F.A.S.); (S.A.A.); (B.A.D.)
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Du S, Huang X, Cai Y, Hao Y, Qiu S, Liu L, Cui M, Luo L. Differential Antioxidant Compounds and Activities in Seedlings of Two Rice Cultivars Under Chilling Treatment. FRONTIERS IN PLANT SCIENCE 2021; 12:631421. [PMID: 33719304 PMCID: PMC7952967 DOI: 10.3389/fpls.2021.631421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/02/2021] [Indexed: 05/15/2023]
Abstract
Variations in antioxidant compounds were examined in seedlings of two rice cultivars (Qiutianxiaoting and 93-11) exposed to low temperature (4°C) for 0, 12, 36, and 48 h. Antioxidant activity was identified by 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP) assays. The concentrations of total phenols, flavonoids, chlorophyll, and anthocyanins (ACNs) were determined by spectrophotometry. In addition, high-performance liquid chromatography (HPLC) was used to reveal the changes in phenolic compound concentrations in rice seedlings under chilling treatment. Results showed that antioxidant concentrations and antioxidant activity after chilling treatment were higher in 93-11 compared to Qiutianxiaoting, reaching the highest level at 36 h chilling treatment in 93-11. Phenolic compounds in Qiutianxiaoting decreased between 12 and 36 h but then increased at 48 h, whereas the corresponding levels in 93-11 increased as chilling time increased. Moreover, 10 phenolic compounds were detected and quantified by HPLC, of which gallic acid and caffeic acid tended to only exist in 93-11, whereas rutin was observed only in Qiutianxiaoting. The results of this study could be leveraged to optimize the antioxidant potential of rice in the context of healthy food choices.
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Affiliation(s)
- Shangguang Du
- School of Life Sciences, Nanchang University, Nanchang, China
- School of Life Sciences, Nanchang Normal University, Nanchang, China
| | - Xueyong Huang
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Yali Cai
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Yingbin Hao
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Shengrong Qiu
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Lihua Liu
- School of Life Sciences, Nanchang University, Nanchang, China
| | - Meng Cui
- School of Life Sciences, Nanchang University, Nanchang, China
- *Correspondence: Meng Cui,
| | - Liping Luo
- School of Life Sciences, Nanchang University, Nanchang, China
- *Correspondence: Meng Cui,
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Baral K, Coulman B, Biligetu B, Fu YB. Advancing crested wheatgrass [Agropyron cristatum (L.) Gaertn.] breeding through genotyping-by-sequencing and genomic selection. PLoS One 2020; 15:e0239609. [PMID: 33031422 PMCID: PMC7544028 DOI: 10.1371/journal.pone.0239609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/09/2020] [Indexed: 11/18/2022] Open
Abstract
Crested wheatgrass [Agropyron cristatum (L.) Gaertn.] provides high quality, highly palatable forage for early season grazing. Genetic improvement of crested wheatgrass has been challenged by its complex genome, outcrossing nature, long breeding cycle, and lack of informative molecular markers. Genomic selection (GS) has potential for improving traits of perennial forage species, and genotyping-by-sequencing (GBS) has enabled the development of genome-wide markers in non-model polyploid plants. An attempt was made to explore the utility of GBS and GS in crested wheatgrass breeding. Sequencing and phenotyping 325 genotypes representing 10 diverse breeding lines were performed. Bioinformatics analysis identified 827, 3,616, 14,090 and 46,136 single nucleotide polymorphism markers at 20%, 30%, 40% and 50% missing marker levels, respectively. Four GS models (BayesA, BayesB, BayesCπ, and rrBLUP) were examined for the accuracy of predicting nine agro-morphological and three nutritive value traits. Moderate accuracy (0.20 to 0.32) was obtained for the prediction of heading days, leaf width, plant height, clump diameter, tillers per plant and early spring vigor for genotypes evaluated at Saskatoon, Canada. Similar accuracy (0.29 to 0.35) was obtained for predicting fall regrowth and plant height for genotypes evaluated at Swift Current, Canada. The Bayesian models displayed similar or higher accuracy than rrBLUP. These findings show the feasibility of GS application for a non-model species to advance plant breeding.
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Affiliation(s)
- Kiran Baral
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bruce Coulman
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Bill Biligetu
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
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Dadjo C, Nyende AB, Yao N, Kiplangat N, Assogbadjo AE. Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology. PLoS One 2020; 15:e0238984. [PMID: 32966312 PMCID: PMC7511007 DOI: 10.1371/journal.pone.0238984] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/27/2020] [Indexed: 11/18/2022] Open
Abstract
Garcinia kola (Heckel) is a versatile tree indigenous to West and Central Africa. All parts of the tree have value in traditional medicine. Natural populations of the species have declined over the years due to overexploitation. Assessment of genetic diversity and population structure of G. kola is important for its management and conservation. The present study investigates the genetic diversity and population structure of G. kola populations in Benin using ultra-high-throughput diversity array technology (DArT) single nucleotide polymorphism (SNP) markers. From the 102 accessions sampled, two were excluded from the final dataset owing to poor genotyping coverage. A total of 43,736 SNPs were reported, of which 12,585 were used for analyses after screening with quality control parameters including Minor allele frequency (≥ 0.05), call rate (≥ 80%), reproducibility (≥ 95%), and polymorphic information content (≥ 1%). Analysis revealed low genetic diversity with expected heterozygosity per population ranging from 0.196 to 0.228. Pairwise F-statistics (FST) revealed low levels of genetic differentiation between populations while an Analysis of molecular variance (AMOVA) indicated that the majority of variation (97.86%) was within populations. Population structure analysis through clustering and discriminant analysis on principal component revealed two admixed clusters, implying little genetic structure. However, the model-based maximum likelihood in Admixture indicated only one genetic cluster. The present study indicated low genetic diversity of G. kola, and interventions are needed to be tailored towards its conservation.
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Affiliation(s)
- Colombe Dadjo
- Institute of Basic Sciences, Technology and Innovation, Pan African University, Nairobi, Kenya
- Laboratory of Applied Ecology, Faculty Agronomic Sciences, University of Abomey-Calavi, Cotonou, Rep. Benin
- * E-mail:
| | - Aggrey B. Nyende
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Nasser Yao
- Bioscience Eastern and Central Africa, International Livestock Research Institute, Nairobi, Kenya
| | - Ngeno Kiplangat
- Animal Breeding and Genomics Group, Department of Animal Science, Egerton University, Egerton, Kenya
| | - Achille E. Assogbadjo
- Laboratory of Applied Ecology, Faculty Agronomic Sciences, University of Abomey-Calavi, Cotonou, Rep. Benin
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Biswas DK, Coulman B, Biligetu B, Fu YB. Advancing Bromegrass Breeding Through Imaging Phenotyping and Genomic Selection: A Review. FRONTIERS IN PLANT SCIENCE 2020; 10:1673. [PMID: 32010160 PMCID: PMC6974688 DOI: 10.3389/fpls.2019.01673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/28/2019] [Indexed: 05/24/2023]
Abstract
Breeding forage crops for high yields of digestible biomass along with improved resource-use efficiency and wide adaptation is essential to meet future challenges in forage production imposed by growing demand, declining resources, and changing climate. Bromegrasses (Bromus spp.) are economically important forage species in the temperate regions of world, but genetic gain in forage yield of bromegrass is relatively low. In particular, limited breeding efforts have been made in improving abiotic stress tolerance and resource-use efficiency. We conducted a literature review on bromegrass breeding achievements and challenges, global climate change impacts on bromegrass species, and explored the feasibility of applying high-throughput imaging phenotyping techniques and genomic selection for further advances in forage yield and quality selection. Overall genetic gain in forage yield of bromegrass has been low, but genetic improvement in forage yield of smooth bromegrass (Bromus inermis Leyss) is somewhat higher than that of meadow bromegrass (Bromus riparius Rehm). This low genetic gain in bromegrass yield is due to a few factors such as its genetic complexity, lack of long-term breeding effort, and inadequate plant adaptation to changing climate. Studies examining the impacts of global climate change on bromegrass species show that global warming, heat stress, and drought have negative effects on forage yield. A number of useful physiological traits have been identified for genetic improvement to minimize yield loss. Available reports suggest that high-throughput imaging phenotyping techniques, including visual and infrared thermal imaging, imaging hyperspectral spectroscopy, and imaging chlorophyll fluorescence, are capable of capturing images of morphological, physiological, and biochemical traits related to plant growth, yield, and adaptation to abiotic stresses at different scales of organization. The more complex traits such as photosynthetic radiation-use efficiency, water-use efficiency, and nitrogen-use efficiency can be effectively assessed by utilizing combinations of imaging hyperspectral spectroscopy, infrared thermal imaging, and imaging chlorophyll fluorescence techniques in a breeding program. Genomic selection has been applied in the breeding of forage species and the applications show its potential in high ploidy, outcrossing species like bromegrass to improve the accuracy of parental selection and improve genetic gain. Together, these new technologies hold promise for improved genetic gain and wide adaptation in future bromegrass breeding.
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Affiliation(s)
- Dilip K. Biswas
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Bruce Coulman
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Bill Biligetu
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada
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